Karoly Bosa, Wolfgang Schreiner, Friedrich Priewasser

@techreport{RISC4018, author = {Karoly Bosa and Wolfgang Schreiner and Friedrich Priewasser}, title = {{Report on the First Feature-Complete Prototype of a Distributed Supercomputing API for the Grid}}, language = {english}, abstract = {In the frame of the Austrian Grid Phase 2, we have designed andimplemented an API for grid computing that can be used for developinggrid-distributed parallel programs without leaving the level ofthe language in which the core application is written. Our softwareframework is able to utilize the information about heterogeneous gridenvironments in order to adapt the algorithmic structure of parallelprograms to the particular situation. Since our solution hides lowlevelgrid-related execution details from the application by providingan abstract execution model, it is able to eliminate some algorithmicchallenges of nowadays grid programming. In this paper, we reporton the first feature-complete prototype of our topology-aware softwaresystem extended with some benchmark results and a performancecomparison between MPICH-G2 and our system.}, number = {AG-D4-1-2010_1}, year = {2010}, month = {March}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, MPICH-G2, Topology-Aware Programming}, sponsor = {Austrian Grid}, length = {18}, type = {Austrian Grid Deliverable}}

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3813, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{A Prototype Implementation of a Distributed Supercomputing API for the Grid}}, language = {english}, abstract = {We proposed to participate in the Austrian Grid Phase 2 within the frame of the activity “Grid Research”. Our goal is to develop a distributed software framework and an API for grid computing which shall empower applications to perform scheduling decisions on their own, utilizing the information about the grid environment in order to adapt the algorithmic structure to the particular situation. The planned solution will be able to eliminate some algorithmic challenges of nowadays grid programming. Since the last report we implemented a prototype version of the proposed API and successfully tested on some resources of the Austrian Grid. In this paper, we present the current state of the implementation and envisage the next development steps.}, number = {AG-D4-1-2009_1}, year = {2009}, month = {March}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, MPICH-G2, Toplogy-Aware Programming}, sponsor = {Austrian Grid}, length = {31}, type = {Austrian Grid Deliverable}}

A Supercomputing API for the Grid

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3887, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{A Supercomputing API for the Grid}}, language = {english}, abstract = {No application can execute efficiently on the grid that is not aware of the fact that it runs in an heterogeneous network environment with heterogeneous nodes. We report on an ongoing work whose goal is to develop a distributed software framework and an API for grid computing which shall empower applications to perform scheduling decisions on their own and utilizing the information about the grid environment in order to adapt their algorithmic structure to the particular situation. Since our solution hides low-level grid-related execution details from the application by providing an abstract execution model, it is able to eliminate some algorithmic challenges of nowadays grid programming.}, year = {2009}, month = {August}, institution = {Austrian Grid}, keywords = {Grid Computing, MPICH-G2, Toplogy-Aware Programming}, sponsor = {Austrian BMBWK (Federal Ministry for Education, Science and Culture) under the contracts GZ 4003/2-VI/4c/2004 and GZ BMWF-10.220/0002-II/10/2007}, length = {4}, type = {Extended Abstract for the 3rd Austrian Grid Symposium, September 28-29, 2009}}

Report on the Second Prototype of a Distributed Supercomputing API for the Grid

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3894, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{Report on the Second Prototype of a Distributed Supercomputing API for the Grid}}, language = {english}, abstract = {We participate in the Austrian Grid Phase 2 within the frame of the activity “Grid Research”. We deal with development of a distributed programming tool for grid computing which shall empower applications to perform scheduling decisions on their own, utilizing the information about the grid environment in order to adapt the algorithmic structure to the particular situation. Our goal is to design and implement a software framework and an API that can be used for developing grid-distributed parallel programs without leaving the level of the language in which the core application is written. The planned solution will be able to eliminate some algorithmic challenges of nowadays grid programming. In this paper, we report on the second prototype of our topology-aware software system extended with the description of our newly developed scheduling algorithm.}, number = {AG-D4-2-2009_1}, year = {2009}, month = {September}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, MPICH-G2, Toplogy-Aware Programming}, sponsor = {Austrian Grid}, length = {20}, type = {Austrian Grid Deliverable}}

Re-engineering of a Grid Aware Medical Database System Based on a Metamodel

Amira Zaki

@mastersthesis{RISC3854, author = {Amira Zaki}, title = {{Re-engineering of a Grid Aware Medical Database System Based on a Metamodel}}, language = {english}, abstract = {Over the last few decades, the amount of medical data available through the advancementsin medical and clinical researches has greatly increased. Therefore, the need for huge storagecapacities, eective data retrieval methods and high performance computations has becomesignicantly important. The aim of this work was to develop a simplied metamodel forSEE++, a software system for the computer-aided simulation of eye motility disorders andtheir treatments. The poor performance of the current over-engineered metamodel was thedriving force behind the necessary enhancements. Thus, the newly developed metamodelallows the integration into a Grid environment to achieve near real-time performance forthe numerous simulations and complex calculations performed. This was done using aninstantiation of YAMM, a tool for creating web-based database applications based on ametamodel, comprising both the data and model conjointly in a relational back-end. Ourwork involved restructuring YAMM to parse its database interactions into a generic formto query any resource. An interoperability layer was created to handle various databaseconnections. The use of a relational back-end was implemented and an interface was designedfor using any other system like a Grid-aware database. Moreover, the methodologyof instantiating YAMM to represent the SEE++ data model was investigated, resulting inthe discovery of a few problems in YAMM's expressiveness, which introduced ambiguity inthe SEE++ data model representation.}, year = {2009}, month = {July}, translation = {0}, school = { Internationaler Universitätslehrgang Informatics: Engineering & Management (ISI Hagenberg)}, length = {65}}

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3400, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{Report on Experiments with Globus 4 and gLite}}, language = {english}, abstract = {In this paper, we compare two implementations of a grid-based softwaresystem on the grid middleware Globus Toolkit 4 and gLite, respectively. This systemcalled “Grid-Enabled SEE++” is a grid-based simulation software that supportsthe diagnosis and treatment of certain eye motility disorders (strabismus). First, wedeveloped a parallel version of the software with the help of Globus 4. Since wemet with some limitations of Globus 4, we also designed and developed a version ofSEE++ based on gLite. We focus on the differences between the initial Globus versionand the gLite version of our software system and report on some comparativebenchmark results.}, number = {AG-D4-1-2007-1}, year = {2008}, month = {January}, note = {Extended Version}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {“Grid-Enabled SEE++”, Grid Applications, Grid Middleware, Globus, gLite}, sponsor = {Austrian Grid}, length = {14}, type = {Austrian Grid Deliverable}}

Report on the State of the Art Survey

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3418, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{Report on the State of the Art Survey}}, language = {english}, abstract = {We proposed to participate in the Austrian Grid Phase 2 within the frame of the activity "Grid Research". We intend to deal with development of a distributed programming tool for grid computing which shall empower applications to perform scheduling decisions on their own, utilizing the information about the grid environment in order to adapt the algorithmic structure to the particular situation. Our goal is to design and implement an API that can be used for developing grid-distributed parallel programs without leaving the level of the language in which the core application is written (C/Fortran/Java). This API will be able to eliminate lots of the algorithmic challenges of nowadays grid programming. In this paper, we summarize our experiences concerning the existing programming tools on the area of the multi-cluster and grid environments.}, number = {AG-D4-1-2008_2}, year = {2008}, month = {March}, note = {Extended Version}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, Grid Middleware, MPICH-G2, GridRPC}, sponsor = {Austrian Grid}, length = {18}, type = {Austrian Grid Deliverable}}

The Porting of a Medical Grid Application from Globus 4 to the gLite Middleware

@inproceedings{RISC3439, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{The Porting of a Medical Grid Application from Globus 4 to the gLite Middleware}}, booktitle = {{Proceedings of DAPSYS 2008}}, language = {english}, abstract = {In this paper, we compare two implementations of a grid-based software system on the grid middleware Globus Toolkit 4 and gLite, respectively. This system called ``Grid-Enabled SEE++'' is a grid-based simulation software that supports the diagnosis and treatment of certain eye motility disorders (strabismus). First, we developed a parallel version of the software with the help of Globus 4. Since we met with some limitations of Globus 4, we also designed and developed a version of SEE++ based on gLite. We focus on the differences between the initial Globus version and the gLite version of our software system and report on some comparative benchmark results.}, pages = {51--61}, publisher = {Springer}, isbn_issn = {ISBN-13: 978-0-387-79447-1}, year = {2008}, month = {September}, editor = {Peter Kacsuk at al.}, refereed = {yes}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, SEE++, gLite}, length = {11}, conferencename = {DAPSYS 2008, 7th INTERNATIONAL CONFERENCE ON DISTRIBUTED AND PARALLEL SYSTEMS}, url = {http://www.lpds.sztaki.hu/dapsys/}}

Initial Design of a Distributed Supercomputing API for the Grid

Karoly Bosa, Wolfgang Schreiner

@techreport{RISC3474, author = {Karoly Bosa and Wolfgang Schreiner}, title = {{Initial Design of a Distributed Supercomputing API for the Grid}}, language = {english}, abstract = {We proposed to participate in the Austrian Grid Phase 2 within the frame of the activity “Grid Research”. We intend to deal with development of a distributed programming tool for grid computing which shall empower applications to perform scheduling decisions on their own, utilizing the information about the grid environment in order to adapt the algorithmic structure to the particular situation. Our goal is to design and implement a software framework and an API that can be used for developing grid-distributed parallel programs without leaving the level of the language in which the core application is written. The planned solution will be able to eliminate some algorithmic challenges of nowadays grid programming. In this paper, we outline our idea concerning the proposed software system and already discuss some implementation details.}, number = {AG-D4-2-2008_1}, year = {2008}, month = {September}, institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, keywords = {Grid Computing, Grid Middleware, MPICH-G2, NWS}, sponsor = {Austrian Grid Project}, length = {34}, type = {Austrian Grid Deliverable}}

Grid-aware Database Support for Medical Software

Imre Zoltan Matko

@mastersthesis{RISC3458, author = {Imre Zoltan Matko}, title = {{Grid-aware Database Support for Medical Software}}, language = {english}, abstract = {SEE-GRID is a research project based on the SEE++ software system for the biomechanical simulation of the human eye. The project aims to develop a Grid-enabled version ofSEE++ to support ophthalmologists in the treatment of common eye motility disorders.Currently there exist Grid-based implementations of computation and calculation services required by SEE++ and a prototype of a metamodel based medical database. The current database implementation has some restrictions, performance problems and its Grid integration is unfinished. The goal of this thesis is to analyze the software and find performance bottlenecks and to extend the design with a Grid interface and provide a prototype implementation.Based on the benchmarking and profiling of the SEE-GRID database components we realized that the current metamodel is too complex, causing to spend most of the runtime with database queries and data transformations. Some feasible solutions we proposed are the simplification of the metamodel or the usage of fast, XML based back-ends.We have evaluated state of the art Grid data-resource management tools and found OGSA-DAI and AMGA two promising solutions for our project. We have extended the design of the SEE-GRID database with a Globus “Web Service Resource Framework” based interface and with the services of OGSA-DAI. To prove the applicability of the design we prototyped the Grid interface and evaluated in practice OGSA-DAI with respect to the needs of SEE-GRID.iv}, year = {2008}, month = {July}, translation = {0}, school = {Internationaler Universitätslehrgang Informatics: Engineering & Management (ISI Hagenberg)}, length = {69}}

Parallel Algorithms for Sparse Matrices in an Industrial Optimization Software

Kenji Miyamoto

@mastersthesis{RISC3459, author = {Kenji Miyamoto}, title = {{Parallel Algorithms for Sparse Matrices in an Industrial Optimization Software}}, language = {english}, abstract = {Optimization problems have an important role in industry, and the finite elementmethod is a popular solution to solve optimization problems numerically. The finiteelement method rely on linear algebra, high performance linear equation solvera arethere important topic in applied science.In this thesis, we study the high performance forward/backward substitution methodby means of parallel computing.We implement various solutions and benchmark each ofthem in detail on two computers with different hardware architectures; one is a sharedmemory multicore machine, and the other one is a multicore machine with virtual sharedmemory machine. We tried two programming models, MPI and POSIX threading, andfind the difference of these programming models by run benchmarks on two computers.We achieve good speedup by integrating some solutions.}, year = {2008}, month = {July}, translation = {0}, school = {Internationaler Universitätslehrgang Informatics: Engineering & Management (ISI Hagenberg)}, length = {92}}

@inproceedings{RISC3433, author = {Dacian Tudor and Vladimir Cretu and Wolfgang Schreiner}, title = {{Designing an Architecture for Distributed Shared Data on the Grid}}, booktitle = {{Algorithms and Architectures for Parallel Processing}}, language = {english}, abstract = {Despite the continuous advances of the last years in grid computing,the grid computing programming paradigms are dominated by the messagepassing concept. There is little support for other paradigms such as shared dataor associative programming. In this paper we analyze some of the existingsolutions for grid shared data programming and highlight some of theirdrawbacks. We propose a new architecture and its core features as well as newevaluation means of its behavior in various scenarios including the nextgeneration grid systems. In addition to the simplicity of our solution, we believethat it would allow us to easily apply further extensions.}, series = {Lecture Notes in Computer Science}, volume = {22}, pages = {261--264}, publisher = {Springer}, isbn_issn = {ISBN 0302-9743}, year = {2008}, editor = {Anu G. Bourgeois and S. Q. Zheng}, refereed = {yes}, keywords = {grid computing, distributed shared data, programming model}, length = {4}, conferencename = {ICA3PP 2008, International Conference on Algorithms and Architectures for Parallel Processing, June 9-11, Agia Napa, Cyprus}}

Investigations on Improving the SEE-GRID Optimization Algorithm

Johannes Watzl

@mastersthesis{RISC3444, author = {Johannes Watzl}, title = {{Investigations on Improving the SEE-GRID Optimization Algorithm}}, language = {english}, abstract = {In this work various ways to accelerate the computation process in the SEEKID/SEE-GRID software for the biomechanical simulation of the human eyeare investigated. Both sequential and parallel strategies are discussed. Toimprove the sequential optimizer, the Broyden update method is utilized. Astrategy to interpolate function values is first found on the basis of the Delaunayalgorithm. An enhanced strategy was developed based on the specialregularity of the mesh used in the interpolation program. The strategies wereimplemented and the results of the benchmarks are presented together withthe source code.}, year = {2008}, month = {June}, translation = {0}, school = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria}, length = {115}}

Experiences on Grid Shared Data Programming

Dacian Tudor, Georgiana Macariu, Wolfgang Schreiner, Vladimir Cretu

@article{RISC3477, author = {Dacian Tudor and Georgiana Macariu and Wolfgang Schreiner and Vladimir Cretu }, title = {{Experiences on Grid Shared Data Programming}}, language = {english}, abstract = {Despite the continuous advances of the last years in grid computing,programming paradigms are dominated by the message passing concept. There is littlesupport for other paradigms such as shared data or associative programming. In this paperwe analyze why previous attempts did not have a significant impact in the grid computingcommunity. We start by assessing the landscape of grid programming solutions with a focuson shared data concepts. Next, we introduce an original idea to attack shared dataprogramming on the grid by making use of both relaxed consistency models and userspecified type consistency in an object oriented model. Last but not least, we present aprototype architecture together with experimental results.}, journal = {Journal of Grid and Utility Computing (IJGUC)}, pages = {43--54}, publisher = {Inderscience}, isbn_issn = {ISSN 1741-847X}, year = {2008}, note = {To appear}, refereed = {yes}, length = {12}}